Pdb2gmx not generating topol.top file

User discussions
1

GROMACS version: 202
GROMACS modification: No
I am trying to simulate a simple organic molecule (chloroethane) using gromacs. I already have a pdb, itp file for it and ran the pdb2gmx command + selection of force fields. I kept running into

Back Off! I just backed up topol.top to ./#topol.top.3#

Processing chain 1 (8 atoms, 1 residues)

Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
9 out of 9 lines of specbond.dat converted successfully

Program: gmx pdb2gmx, version 2024.2-Homebrew
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 616)

Fatal error:
Residue ‘LIG’ not found in residue topology database

I think maybe this is because of me running an organic molecule? And unfortunately it does not produce the topol.top file that i need for me to run the next steps (ie. solvation). Can anyone please help out? Thnks!

2

I think you need to first make the .itp file of your organic molecule by using some website like swissparam and then you can read the instructions given below as to how to incorporate these parameters in gromacs . If you have incorporated your .itp file correctly , i dont think you should find any trouble